Non-small cell lung cancer (NSCLC) is the most common type of bronchogenic carcinoma. Although chemotherapeutic regimens with greater efficacy continue to be developed, the best regimens presently give an overall regression rate of only 30-50%. This lack of response is attributable to resistance that is present de novo or develops in response to treatment. It is believed that mechanisms of chemoresistance likely involve multiple gene products. It is important to define the role of specific genes involved in tumor development and growth and to identify and quantify those genes and gene products that can serve as targets for diagnosis, prevention, monitoring and treatment of cancer.
In certain instances, therapeutic agents that are initially effective become ineffective or less effective for a patient over time. The same therapeutic agent can continue to be effective for a longer period of time for a different patient. Further, the therapeutic agents can be ineffective or harmful to still other patients. Therefore, it would be beneficial to identify genes and/or gene products that could serve as markers with respect to cancers and to given therapeutic agents. The ability to make such predictions and corrections in the treatment make it possible to more accurately make decisions on the therapeutic regime at an earlier stage in time in the course of a treatment of a patient.
Currently, cisplatin and carboplatin are among the most widely used cytotoxic anticancer drugs. However, resistance to these drugs through de novo or induced mechanisms undermines their curative potential. Perez, R. P., Cellular and molecular determinants of cisplatin resistance, Eur. J. Cancer (1998), 34, 1535-1542. Recently, understanding regarding potential modes of chemoresistance to platinum compounds has been obtained through studies correlating cytotoxicity with nucleotide excision-repair (NER) (Dijt, F., Fitchinger-Schepman, A. M., Berends, F., Reedikj, J., Formation and repair of cisplatin-induced adducts to DNA in cultured normal and repair-deficient human fibroblasts, Cancer Res. (1988), 48, 6058-6062. Zamble, D. B., Lippard, S. J., Cisplatin and DNA repair in cancer chemotherapy, Trends Biochem Sci (1995), 20, 435-439. States, J. C., Reed, E., Enhanced XPA mRNA levels in cisplatin-resistant human ovarian cancer are not associated with XPA mutations or gene amplifications, Cancer Lett. (1996), 108, 233-237. Ferry, K. V., Fink, D., Johnson, S. W., Hamilton, T. C., Howell, S. B., Quantitation of platinum-DNA adduct repair in mismatch repair deficient and proficient human colorectal cancer cell lines using an in vitro DNA repair assay, Proc. Am. Assoc. Cancer Res. (1997), abstract, 38, 359. Jordan, P., Carmo-Fonseca, M., Molecular mechanisms involved in cisplatin cytotoxicity, Cell Mol. Life Sci. (2000), 57, 1229-1235. Kartalou, M., Essingmann, J. M., Mechanisms of resistance to cisplatin, Mutat. Res. (2001), 478, 23-43) or drug uptake/efflux (Kartalou, M., Essingmann, J. M., Mechanisms of resistance to cisplatin, Mutat. Res. (2001), 478, 23-43. Berger, W., Elbling, L., Hauptmann, E., Micksche, M., Expression of the multidrug resistance-associated protein (MRP) and chemoresistance of human non-small-cell lung cancer cells, Int. J. Cancer (1997), 73, 84-93. Borst, P., Kool, M., Evers, R., Do cMOAT (MRP2), other MRP homologues, and LRP play a role in MDR? Cancer Biol. (1997), 8, 205-213. Young, L. C., Campling, B. G., Voskoglou-Nomikos, T., Cole, S. P. C., Deeley, R. G., Gerlach, J. H., Expression of multidrug resistance protein-related genes in lung cancer: correlation with drug response, Clin. Cancer Res. (1999), 5, 673-480. Berger, W., Elbling, L., Micksche, M., Expression of the major vault protein LRP in human non-small-cell lung cancer cells: activation by short-term exposure to antineoplastic drugs, Int. J. Cancer (2000), 88, 293-300. Borst, P., Evers, R., Kool, M., Wijnholds, J., A family of drug transporters: the multidrug resistance-associated proteins, J Nat. Cancer Inst. (2000), 92, 1295-1302. Oguri, T., Isobe, T., Suzuki, T., Nishio, K., Fujiwara, Y., Katoh, O., Yamakido, M., Increased expression of the MRP5 gene is associated with exposure to platinum drugs in lung cancer, Int. J. Cancer (2000), 86, 95-100.
Current advances in technology, including microarrays and quantitative RT-PCR methods, are allowing classification of cancer types on the basis of functional genomics as opposed to histomorphology. Golub, T. R., Slonim, D. K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J. P., Coller, H., Loh, M. L., Downing, J. R., Caligiuri, M. A., Bloomfield, C. D., Lander, E. S., Molecular classification of cancer: class discovery and class prediction by gene expression monitoring, Science (1999), 286, 531-537. Alizadeh, A. A., Eisen, M. B., Davis, R. E., Ma, C., Lossos, I. S., Rosenwald, A., Boldrick, J. C., Sabet, H., Tran, T., Yu, X., Powell, J. I., Yang, L., Marti, G. E., Moore, T., Hudson, Jr., J., Lu, L., Lewis, D. B., Tibshirani, R., Sherlock, G., Chan, W. C., Greiner, T. C., Weisenburger, D. D., Armitage, J. O., Warnke, R., Staudt, L. M., et al., Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling, Nature (2000), 403, 503-511. For example, they may allow for the discovery of predictive markers based on gene expression profiles. Microarray screening analysis currently is being investigated to predict chemotherapeutic sensitivity based on gene expression profiles. Scherf, U., Ross, D. T., Waltham, M., Smith, L. H., Lee, J. K., Tanabe, L., Kohn, K. W., Reinhold, W. C., Myers, T. G., Andrews, D. T., Scudiero, D. A., Eisen, M. B., Sausville, E. A., Pommier, Y., Botstein, D., Brown, P. O., Weinstein, J. N., A gene expression database for the molecular pharmacology of cancer, Nat. Genet. (2000), 24, 236-244. Kihara, C. Tsunoda, T., Tanaka, T., Yamana, H., Furukawa, Y., Ono, K., Kitahara, O., Zembutsu, H., Yanagawa, R., Hirata, K., Takagi, T., Nakamura, Y., Prediction of sensitivity of esophageal tumors to adjuvant chemotherapy by cDNA microarray analysis of gene-expression profiles, Cancer Res. (2001), 61, 6474-6479. Zembutsu, H., Ohnishi, Y., Tsunoda, T., Furukawa, Y., Katagiri, T., Ueyama, Y., Tamaoki, N., Nomura, T., Kitahara, O., Yanagawa, R., Hirata, K., Nakamura, Y., Genome-wide cDNA microarray screening to correlate gene expression profiles with sensitivity of 85 human cancer xenografts to anticancer drugs, Cancer Res. (2002), 62, 518-527. An advantage of microarray analysis is that thousands of genes may be simultaneously evaluated. However, it is generally recognized that, due to lack of standardization, relatively low sensitivity and relatively poor lower thresholds of detection, microarray assessments need to be confirmed with follow-up quantitative methods. StaRT-PCR is a method that allows for rapid, reproducible, standardized, quantitative measurements for many genes simultaneously. Willey, J. C., Crawford, E. L., Jackson, C. M., Weaver, D. A., Hoban, J. C., Khuder, S. A., DeMuth, J. P., Expression measurement of many genes simultaneously by quantitative RT-PCR using standardized mixtures of competitive templates, Am. J. Respir. Cell Mol. Biol. (1998), 19, 6-17. Weaver, et al. Comparison of expression patterns by microarray and standardized RT-PCR analyses in lung cancer cell lines with varied sensitivity to carboplatin. Proc. Am. Assoc. Cancer Res. 2001 (abstract) 42, 606.
StaRT-PCR can also be used to more accurately diagnose lung cancer in small biopsy tissues. Warner, et al. “High c-myc×E2F-1/p21 may augment cytologic diagnosis of NSCLC” Prod. Am. Assoc. Cancer Res. Vol. 43, abstract 3738, March 2002; Weaver, et al. Gene expression modeling of cisplatin chemoresistance in non-small cell lung cancer cell lines utilizing standardized RT StarRT-PCR” Prod. Am. Assoc. Cancer Res. Vol. 43, abstract 5471, March 2002.